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prov-to-sql-tsp.sh
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#!/bin/bash
export RUNID=$(basename $1 .log)
export WFID="${RUNID}:"
# TODO is there already a URI form for identifying workflows?
export WF="${RUNID}"
echo "Generating SQL for $RUNID:"
# this gives a distinction between the root process for a workflow and the
# workflow itself. perhaps better to model the workflow as a process
echo " - Root thread."
echo "INSERT INTO fun_call (id, type, name, run_id) VALUES ('${WFID}0', 'rootthread', '$RUNID', '$WF');" >> /tmp/$RUNID.sql
echo " - Function calls."
while read time duration thread localthread endstate tr_name scratch; do
id=$(echo "$thread" | sed "s/execute\://")
echo "INSERT INTO fun_call (id, type, run_id) VALUES ('$id', 'execute', '$WF');" >> /tmp/$RUNID.sql
echo "INSERT INTO app_fun_call (id, name, start_time, duration, final_state, scratch) VALUES ('$id', '$tr_name', $time, $duration, '$endstate', '$scratch');" >> /tmp/$RUNID.sql
done < execute.global.event
echo " - Application executions."
while read start_time duration globalid id endstate thread site scratch; do
# cut off the last component of the thread, so that we end up at the
# parent thread id which should correspond with the execute-level ID
inv_id="$WFID$(echo $thread | sed 's/-[^-]*$//')"
eid=$(echo "$globalid" | sed "s/execute2\://")
echo "INSERT INTO app_exec (id, app_fun_call_id, start_time, duration, final_state, site) VALUES ('$eid', '$inv_id', $start_time, $duration, '$endstate', '$site');" >> /tmp/$RUNID.sql
done < execute2.global.event
echo " - Mapped variables."
while read dataset filename; do
echo "INSERT INTO ds (id) VALUES ('$dataset');" >> /tmp/$RUNID.sql
echo "INSERT INTO mapped (id, filename) VALUES ('$dataset', '$filename');" >> /tmp/$RUNID.sql
done < dataset-filenames.txt
echo " - Primitive variables."
while read dataset idtype equal value rest; do
echo "INSERT INTO ds (id) VALUES ('$dataset');" >> /tmp/$RUNID.sql
echo "INSERT INTO primitive (id, value) VALUES ('$dataset', '$value');" >> /tmp/$RUNID.sql
done < dataset-values.txt
echo " - Arrays and structures."
while read outer inner; do
echo "INSERT INTO ds (id) VALUES ('$outer');" >> /tmp/$RUNID.sql
echo "INSERT INTO ds (id) VALUES ('$inner');" >> /tmp/$RUNID.sql
echo "INSERT INTO dataset_containment (out_id, in_id) VALUES ('$outer', '$inner');" >> /tmp/$RUNID.sql
cid=$(echo $outer | awk -F "-" '{print $3}')
echo "INSERT INTO fun_call (id, type, name, run_id) VALUES ('${WFID}$cid', 'constructor', 'constructor', '$WF');" >> /tmp/$RUNID.sql
echo "INSERT INTO dataset_in (function_call_id, dataset_id, parameter) VALUES ('${WFID}$cid', '$inner', 'element');" >> /tmp/$RUNID.sql
echo "INSERT INTO dataset_out (function_call_id, dataset_id, parameter) VALUES ('${WFID}$cid', '$outer', 'collection');" >> /tmp/$RUNID.sql
done < tie-containers.txt
echo " - Operator calls."
while read col1 col2 col3 col4 col5 thread name lhs rhs result; do
thread=$(echo $thread | awk 'BEGIN { FS = "=" }; {print $2}')
name=$(echo $name | awk 'BEGIN { FS = "=" }; {print $2}')
lhs=$(echo $lhs | awk 'BEGIN { FS = "=" }; {print $2}')
rhs=$(echo $rhs | awk 'BEGIN { FS = "=" }; {print $2}')
result=$(echo $result | awk 'BEGIN { FS = "=" }; {print $2}')
operatorid="${WFID}operator:$thread"
echo "INSERT INTO ds (id) VALUES ('$lhs');" >> /tmp/$RUNID.sql
echo "INSERT INTO ds (id) VALUES ('$rhs');" >> /tmp/$RUNID.sql
echo "INSERT INTO ds (id) VALUES ('$result');" >> /tmp/$RUNID.sql
echo "INSERT INTO fun_call (id, type, name, run_id) VALUES ('$operatorid', 'operator', '$name', '$WF');" >> /tmp/$RUNID.sql
echo "INSERT INTO dataset_in (function_call_id, dataset_id, parameter) VALUES ('$operatorid', '$lhs', 'lhs');" >> /tmp/$RUNID.sql
echo "INSERT INTO dataset_in (function_call_id, dataset_id, parameter) VALUES ('$operatorid', '$rhs', 'rhs');" >> /tmp/$RUNID.sql
echo "INSERT INTO dataset_out (function_call_id, dataset_id, parameter) VALUES ('$operatorid', '$result', 'result');" >> /tmp/$RUNID.sql
done < operators.txt
echo " - Built-in function calls."
while read id name output; do
echo "INSERT INTO ds (id) VALUES ('$output');" >> /tmp/$RUNID.sql
echo "INSERT INTO fun_call (id, type, name, run_id) VALUES ('$id', 'function', '$name', '$WF');" >> /tmp/$RUNID.sql
echo "INSERT INTO dataset_out (function_call_id, dataset_id, parameter) VALUES ('$id', '$output', 'result');" >> /tmp/$RUNID.sql
done < functions.txt
while read id value; do
echo "INSERT INTO ds (id) VALUES ('$value');" >> /tmp/$RUNID.sql
echo "INSERT INTO dataset_in (function_call_id, dataset_id, parameter) VALUES ('$id', '$value', 'undefined');" >> /tmp/$RUNID.sql
done < function-inputs.txt
echo " - Script run events."
while read start duration wfid rest; do
echo "UPDATE run SET start_time=$start WHERE id='$WF';" >> /tmp/$RUNID.sql
echo "UPDATE run SET duration=$duration WHERE id='$WF';" >> /tmp/$RUNID.sql
done < workflow.event
# TODO this could merge with other naming tables
echo " - Compound functions."
while read start duration thread final_state procname ; do
if [ "$duration" != "last-event-line" ]; then
compoundid=$WFID$thread
echo "INSERT INTO fun_call (id, type, name, run_id) VALUES ('$compoundid', 'compound', '$procname', '$WF');" >> /tmp/$RUNID.sql
fi
done < compound.event
while read start duration thread final_state procname ; do
if [ "$duration" != "last-event-line" ]; then
fqid=$WFID$thread
echo "INSERT INTO fun_call (id, type, name, run_id) VALUES ('$fqid', 'internal', '$procname', '$WF');" >> /tmp/$RUNID.sql
fi
done < internalproc.event
while read t ; do
thread="${WFID}$t"
echo "INSERT INTO fun_call (id, type, name, run_id) VALUES ('$thread', 'scope', 'scope', '$WF');" >> /tmp/$RUNID.sql
done < scopes.txt
echo " - Dataset consumption and production."
while read thread direction dataset variable rest; do
if [ "$direction" == "input" ] ; then
table=dataset_in
else
table=dataset_out
fi
echo "INSERT INTO ds (id) VALUES ('$dataset');" >> /tmp/$RUNID.sql
echo "INSERT INTO $table (function_call_id, dataset_id, parameter) VALUES ('$thread', '$dataset', '$variable');" >> /tmp/$RUNID.sql
done < tie-data-invocs.txt
echo " - Wrapper log resource consumption info."
if [ -f runtime.txt ]; then
while read execute2_id runtime; do
real_secs=$(echo $runtime | awk -F "," '{print $1}' | awk -F ":" '{print $2}')
kernel_secs=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
user_secs=$(echo $runtime | awk -F "," '{print $3}' | awk -F ":" '{print $2}')
percent_cpu=$(echo $runtime | awk -F "," '{print $3}' | awk -F ":" '{print $2}')
max_rss=$(echo $runtime | awk -F "," '{print $3}' | awk -F ":" '{print $2}')
avg_rss=$(echo $runtime | awk -F "," '{print $6}' | awk -F ":" '{print $2}')
avg_tot_vm=$(echo $runtime | awk -F "," '{print $7}' | awk -F ":" '{print $2}')
avg_priv_data=$(echo $runtime | awk -F "," '{print $8}' | awk -F ":" '{print $2}')
avg_priv_stack=$(echo $runtime | awk -F "," '{print $9}' | awk -F ":" '{print $2}')
avg_shared_text=$(echo $runtime | awk -F "," '{print $10}' | awk -F ":" '{print $2}')
page_size=$(echo $runtime | awk -F "," '{print $11}' | awk -F ":" '{print $2}')
major_pgfaults=$(echo $runtime | awk -F "," '{print $12}' | awk -F ":" '{print $2}')
minor_pgfaults=$(echo $runtime | awk -F "," '{print $13}' | awk -F ":" '{print $2}')
swaps=$(echo $runtime | awk -F "," '{print $14}' | awk -F ":" '{print $2}')
invol_context_switches=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
vol_waits=$(echo $runtime | awk -F "," '{print $15}' | awk -F ":" '{print $2}')
fs_reads=$(echo $runtime | awk -F "," '{print $16}' | awk -F ":" '{print $2}')
fs_writes=$(echo $runtime | awk -F "," '{print $17}' | awk -F ":" '{print $2}')
sock_recv=$(echo $runtime | awk -F "," '{print $18}' | awk -F ":" '{print $2}')
sock_send=$(echo $runtime | awk -F "," '{print $19}' | awk -F ":" '{print $2}')
signals=$(echo $runtime | awk -F "," '{print $20}' | awk -F ":" '{print $2}')
exit_status=$(echo $runtime | awk -F "," '{print $21}' | awk -F ":" '{print $2}')
echo "UPDATE app_exec SET real_secs='$real_secs', kernel_secs='$kernel_secs', user_secs='$user_secs', percent_cpu='$percent_cpu', max_rss='$max_rss', avg_rss='$avg_rss', avg_tot_vm='$avg_tot_vm', avg_priv_data='$avg_priv_data', avg_priv_stack='$avg_priv_stack', avg_shared_text='$avg_shared_text', page_size='$page_size', major_pgfaults='$major_pgfaults', minor_pgfaults='$minor_pgfaults', swaps='$swaps', invol_context_switches='$invol_context_switches', vol_waits='$vol_waits', fs_reads='$fs_reads', fs_writes='$fs_writes', sock_recv='$sock_recv', sock_send='$sock_send', signals='$signals', exit_status='$exit_status' WHERE id='$execute2_id';" >> /tmp/$RUNID.sql
#echo "INSERT INTO rt_info (app_exec_id, timestamp, cpu_usage, max_phys_mem, max_virt_mem, io_read, io_write) VALUES ('$execute2_id', $timestamp, $cpu_usage, $max_phys_mem, $max_virtual_mem, $io_read_bytes, $io_write_bytes);" >> /tmp/$RUNID.sql
# for key in $(echo maxrss walltime systime usertime cpu fsin fsout timesswapped socketrecv socketsent majorpagefaults minorpagefaults contextswitchesinv contextswitchesvol); do
# value=$(echo $runtime | awk -F "," '{print $1}' | awk -F ":" '{print $2}')
# echo "INSERT INTO annot_app_exec_num VALUES ('$execute2_id','$key',$value)" >> /tmp/$RUNID.sql
# done
done < runtime.txt
fi
echo " - Function call names."
while read thread appname; do
echo "UPDATE fun_call SET name='$appname' WHERE id='$thread';" >> /tmp/$RUNID.sql
done < invocation-procedure-names.txt
echo " - Wrapper log extra info."
if [ -f extrainfo.txt ]; then
while read execute2_id extrainfo; do
echo $extrainfo | awk -F ";" '{ for (i = 1; i <= NF; i++)
print $i
}' | awk -F "=" '{ print $1 " " $2 }' | awk -F ":" '{ print $1 " " $2 }' > fields.txt
id=$($SQLCMD --tuples-only -c "select app_fun_call_id from app_exec where id='$execute2_id';" | awk '{print $1}')
while read name type value; do
if [ "$type" = "num" ]; then
echo "INSERT INTO annot_app_exec_num (id, name, value) VALUES ('$id', '$name', $value);" >> /tmp/$RUNID.sql
fi
if [ "$type" = "txt" ]; then
echo "INSERT INTO annot_app_exec_text (id, name, value) VALUES ('$id', '$name', '$value');" >> /tmp/$RUNID.sql
fi
done < fields.txt
done < extrainfo.txt
fi
echo " - Prospective provenance (script, tc, sites)."
script_hash=$(openssl dgst -sha1 script.txt | awk '{ print $2 }')
EXISTING=$($SQLCMD --tuples-only -c "select count(*) from script where hash_value='$script_hash';")
if [ "$EXISTING" -eq "0" ]; then
content=$(cat script.txt | sed "s/'/''/g")
echo "INSERT INTO script VALUES ('$script_hash', '$content');" >> /tmp/$RUNID.sql
fi
echo "UPDATE run SET script_hash='$script_hash' WHERE id='$WF';" >> /tmp/$RUNID.sql
tc_hash=$(openssl dgst -sha1 tc.txt | awk '{ print $2 }')
EXISTING=$($SQLCMD --tuples-only -c "select count(*) from tc_file where hash_value='$tc_hash';")
if [ "$EXISTING" -eq "0" ]; then
content=$(cat tc.txt | sed "s/'/''/g")
echo "INSERT INTO tc_file VALUES ('$tc_hash', '$content');" >> /tmp/$RUNID.sql
fi
echo "UPDATE run SET tc_file_hash='$tc_hash' WHERE id='$WF';" >> /tmp/$RUNID.sql
sites_hash=$(openssl dgst -sha1 sites.txt | awk '{ print $2 }')
EXISTING=$($SQLCMD --tuples-only -c "select count(*) from sites_file where hash_value='$sites_hash';")
if [ "$EXISTING" -eq "0" ]; then
content=$(cat sites.txt | sed "s/'/''/g")
echo "INSERT INTO sites_file VALUES ('$sites_hash', '$content');" >> /tmp/$RUNID.sql
fi
echo "UPDATE run SET sites_file_hash='$sites_hash' WHERE id='$WF';" >> /tmp/$RUNID.sql
specification_sig=$(cat /tmp/specification.txt.sig | sed "s/'/''/g")
echo "INSERT INTO annot_script_run_text VALUES ('$RUNID', 'specification_signature', '$specification_sig');" > /tmp/$RUNID-KAIROS.sql
specification_ts=$(uuencode -m /tmp/specification.txt.sig.tsr specification.txt.sig.tsr.base64)
echo "INSERT INTO annot_script_run_text VALUES ('$RUNID', 'specification_timestamp', '$specification_ts');" >> /tmp/$RUNID-KAIROS.sql
parameters_sig=$(cat /tmp/parameters.txt.sig | sed "s/'/''/g")
echo "INSERT INTO annot_script_run_text VALUES ('$RUNID', 'parameters_sig', '$parameters_sig');" >> /tmp/$RUNID-KAIROS.sql
parameters_ts=$(uuencode -m /tmp/parameters.txt.sig.tsr parameters.txt.sig.tsr.base64)
echo "INSERT INTO annot_script_run_text VALUES ('$RUNID', 'parameters_timestamp', '$parameters_ts');" >> /tmp/$RUNID-KAIROS.sql
echo "Finished SQL generation."
echo "Securely timestamping provenance trace."
openssl smime -in /tmp/$RUNID.sql -out /tmp/$RUNID.sql.sig -sign -signer /home/lgadelha/Dropbox/implementacao-dsc/ca/user.pem -inkey /home/lgadelha/Dropbox/implementacao-dsc/ca/user.key
retrospective_sig=$(cat /tmp/$RUNID.sql.sig | sed "s/'/''/g")
echo "INSERT INTO annot_script_run_text VALUES ('$RUNID', 'retrospective_signature', '$retrospective_sig');" >> /tmp/$RUNID-KAIROS.sql
openssl ts -query -data /tmp/$RUNID.sql.sig -out /tmp/$RUNID.sql.sig.tsq -config /home/lgadelha/Dropbox/implementacao-dsc/ca/openssl.conf
openssl ts -reply -queryfile /tmp/$RUNID.sql.sig.tsq -out /tmp/$RUNID.sql.sig.tsr -config /home/lgadelha/Dropbox/implementacao-dsc/ca/openssl.conf
retrospective_ts=$(uuencode -m /tmp/$RUNID.sql.sig.tsr $RUNID.sql.sig.tsr.base64)
echo "INSERT INTO annot_script_run_text VALUES ('$RUNID', 'retrospective_timestamp', '$retrospective_ts');" >> /tmp/$RUNID-KAIROS.sql
echo "Exporting provenance to database..."
$SQLCMD -f /tmp/$RUNID.sql 1> /dev/null 2> /tmp/$RUNID-provenancedb-error.log
$SQLCMD -f /tmp/$RUNID-KAIROS.sql 1> /dev/null 2> /tmp/$RUNID-KAIROS-provenancedb-error.log
mv /tmp/$RUNID.sql /tmp/$RUNID.sql-$(date +%Y%m%d%H%M%S)
echo "Finished exporting provenance to database."